Genomic and enzymatic signatures underlying lifestyle diversity in Xanthomonas arboricola

Xanthomonas arboricola is a plant-associated bacterial species that comprises the pathovars pruni (Xap), juglandis (Xaj), corylina (Xac), which are of high economic concern; and the pathovars arracaciae, celebensis, fragariae and zantedeschiae, which are less relevant, meaning they have a lower economic impact, are less widely distributed, or cause less severe diseases in their host plants. Moreover, the species also includes strains without pathovar affiliation. The pathogenicity of the less economically relevant pathovars as well as the non-affiliated strains has been debated. The present study analysed all the X. arboricola genomes deposited in GenBank by March 2025, focusing on type III secretion system (T3SS), type III effectors (T3Es), cell wall-degrading enzymes (CWDE), amylases and hydrolytic activity.The average nucleotide identity analysis showed that strains belonging to the three main pathovars clustered according to their pathovar designation, harbouring both T3SS and a large T3Es repertoire. However, strains belonging to pathovars of lower economic relevance or with no pathovar affiliation were clustered into two groups, G1 and G2. Remarkably, strains belonging to these less relevant pathovars were scattered along these two groups, exhibiting notable genetic diversity. Moreover, strains in G1 generally displayed T3SS but a limited set of T3Es, whereas strains in G2 lacked a T3SS and exhibited an even more reduced T3Es repertoire. Regarding CWDE, differences in the amount and profiles of cellulolytic, hemicellulolytic and pectinolytic enzymes were observed. While Xap and Xaj possessed the highest counts of hemicellulolytic enzymes, strains in G1 and G2 harboured the highest numbers of cellulolytic and pectinolytic enzymes. Moreover, hydrolytic activities were assayed in a set of strains comprising the three main pathovars and G1 and G2 clusters. It was demonstrated that G1 and G2 strains caused soft rot in pepper fruits, while the main pathovars did not. Furthermore, all the X. arboricola strains analysed hydrolysed starch, except for Xap, which also harboured a reduced set of amylolytic enzymes. The doubtful, atypical or weak pathogenicity, the genomic diversity, the limited content of T3Es, together with the soft rot capacity, the higher counts of cellulolytic and pectinolytic enzymes and the literature, suggest that strains in G1 and G2 would probably be commensal or saprophytic strains that may behave as opportunistic pathogens under certain conditions.